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- PDB-4y00: Crystal Structure of Human TDP-43 RRM1 Domain with D169G Mutation... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4y00 | |||||||||
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Title | Crystal Structure of Human TDP-43 RRM1 Domain with D169G Mutation in Complex with an Unmodified Single-stranded DNA | |||||||||
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![]() | DNA BINDING PROTEIN/DNA / RNA recognition motif 1 Complex / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | ![]() nuclear inner membrane organization / interchromatin granule / perichromatin fibrils / 3'-UTR-mediated mRNA destabilization / 3'-UTR-mediated mRNA stabilization / intracellular non-membrane-bounded organelle / negative regulation by host of viral transcription / pre-mRNA intronic binding / response to endoplasmic reticulum stress / RNA splicing ...nuclear inner membrane organization / interchromatin granule / perichromatin fibrils / 3'-UTR-mediated mRNA destabilization / 3'-UTR-mediated mRNA stabilization / intracellular non-membrane-bounded organelle / negative regulation by host of viral transcription / pre-mRNA intronic binding / response to endoplasmic reticulum stress / RNA splicing / negative regulation of protein phosphorylation / molecular condensate scaffold activity / mRNA 3'-UTR binding / regulation of protein stability / regulation of circadian rhythm / positive regulation of insulin secretion / mRNA processing / positive regulation of protein import into nucleus / cytoplasmic stress granule / rhythmic process / regulation of gene expression / double-stranded DNA binding / regulation of apoptotic process / amyloid fibril formation / regulation of cell cycle / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / lipid binding / mitochondrion / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Chiang, C.H. / Kuo, P.H. / Yang, W.Z. / Yuan, H.S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural analysis of disease-related TDP-43 D169G mutation: linking enhanced stability and caspase cleavage efficiency to protein accumulation Authors: Chiang, C.H. / Grauffel, C. / Wu, L.S. / Kuo, P.H. / Doudeva, L.G. / Lim, C. / Shen, C.K. / Yuan, H.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.3 KB | Display | ![]() |
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PDB format | ![]() | 118.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.6 KB | Display | ![]() |
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Full document | ![]() | 484.9 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 18.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4y0fC ![]() 4iufS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12006.710 Da / Num. of mol.: 4 / Fragment: UNP residues 101-191 / Mutation: D169G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: DNA chain | Mass: 3091.026 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.05 M CH3COONH4, pH 5.0, 15% v/v Jeffamine ED-2001, pH 7.0 PH range: 5.0-7.0 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jan 4, 2014 |
Radiation | Monochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→16.85 Å / Num. all: 11934 / Num. obs: 10669 / % possible obs: 97.86 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.061 / Rsym value: 0.049 / Net I/σ(I): 18.05 |
Reflection shell | Resolution: 2.899→3.003 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.5085 / Mean I/σ(I) obs: 5.96 / % possible all: 100 |
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Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 4IUF Resolution: 3→16.847 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.77 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→16.847 Å
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Refine LS restraints |
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LS refinement shell |
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